Trouble in Tokyo
by Mr-Worth-A-Read
Summary: When the TARDIS malfunctions, the 13th Doctor and her friends are stranded in a Parallel Universe Japan under siege by Godzilla. However as they soon find out, the King of the Monsters isnt the only threat as a nightmare from the Doctor's past has returned with a vengence. And now all hell is about to break loose...(Rated T for mild language and violence)
1. Off to a Flying Start

Chapter 1: Off to a flying start

"Trust me when I say this." the Doctor said as she hopped around to another portion of the TARDIS' console. "You're gonna love it." The ancient machine's time rotor began to whir as the blue box outside dematerialised from corner of the team's home base; aka Graham's front room.

"I've been a few times now and it never gets old."

They were off to explore the Baskhur Islands; a massive cluster of habitable crystalline conglomerates orbiting a gas giant. By the year 200,147, the islands were a popular tourist resort sprawling with holidaymakers from across known space. It was the go-to destination for spacefaring families and wealthy celebrities alike. The only problem was getting there, as the star system was enclosed in a pocket of a harsh nebula.

Luckily, the Doctor knew a shortcut.

Everyone knew what they had to do and when; Ryan had his hands on the multi-vertical Tacitron Compressor switch, Yaz hovered over a keypad ready to upload the bypass codes for the Core System Matrix and Graham stood ready by the lever of the Helmic Regulator. The Doctor kept an eye on the countdown on the screen next to her, ready to give the signal. In order to safely and quickly get through the nebula, the 'shortcut' required the complex procedure to happen in sequence right at the exact moment the TARDIS was transitioning from the T Vortex back to normal space.

"On three. -Just like we practiced, gang." Everyone looked to the screen as the Doctor swung it round for everyone to see before taking her place.

03

02

01

"Here we go!"

All in the span of under five seconds;

The Doctor started the dematerialisation,

Yaz uploaded the override,

Ryan flipped the compressor switch,

And Graham floored the Helmic Regulator

The time rotor in the centre of the console moved up and down as the ship's engines groaned and echoed. It sounded like it was working. The screen blinked with updates as the semi-solid blue box phased through the otherwise impassible nebula.

"See, I told you it would work." Yaz said to Ryan. "We pulled it off."

The two smiled as the Doctor finished wrestling the controls.

"That went better than expected." The Doctor beamed

The violent explosion that shook the TARDIS disagreed.

Sparks burst out of the console, causing everyone to jump back as flames belched out of the ceiling vents above the time rotor. The sound of the engines warped in pitch as if in distress as the four were violently thrown side to side. The purple swirling mirage that was the time vortex vanished into blackness around the TARDIS, followed by space itself. A sense of weightlessness took over the four time travellers as it felt as if they were falling.

"This is why I don't like taking shortcuts!" Graham shouted with a tone of 'I-told-you-so'

"Just shut up and grab onto something!" Ryan snapped back, gripping the handrail on the outer edge of the console.

Anticipating the inevitable impact, the doctor slammed her eyes shut,

"Hang on, everyone!" She shouted as the faint whistling of the approaching ground grew into a nightmarish scream.

The TARDIS was plunged into blackness as the various light sources went dead and the ship shuddered fiercely, throwing the group to the floor. An almost deafening BANG echoed up and down the large circular room before quickly fading.

There was total silence throughout the massive craft; the engines were quiet and not even the distant gong of the cloister bell could be heard.

At first, Graham thought he was dead. It was almost pitch black in the console room as the warm inviting glow of the TARDIS interior was completely gone. Slowly and painfully forcing himself up to a sitting position, Graham's eyes slowly began to adapt to the low light and he could make out the shadowy arches of the surrounding TARDIS console crystals, robbed of their orange light.

The distant clang of metal hitting the floor let him know his hearing had not left him.

"Is everyone alright?" He finally managed to make out.

There was the sound of coughing nearby.

"Yeah, Im alive." Ryan said, catching his breath.

Yaz was puli]king herself to her feet using the console,

"I'm okay, too."

"Doc?"

No answer.

The three exchanged worried glances. Ryan called out this time, but once again, there was no reply from the other side of the TARDIS. Helping his Grandfather to his feet, Ryan staggered around the circular platform, still struggling to make shapes out in the dark.

A head slowly rose up on the other side of the console.

Even in the low light, it was clear to see the Doctor's expression. The dreaded realisation was slowly flooding in.

"It's' dead." She spoke, voice still slightly shaken. "The TARDIS is completely dead."

"What do you mean?" Ryan asked, perplexed.

Standing, the Doctor pressed several button and switches, but the ancient machine did nothing. Looking over, she found the culprit. She had held down the power diversion switch too long; it was still locked in place.

Slamming it back over with a defeated sigh, the Doctor could barely look up at her friends.

"I messed up. I forgot to revert the power and we were pulled out of the time vortex into the void. I'm sorry."

"I thought you said the TARDIS always has access to power." Yaz asked.

"When it's in its own universe." The Doctor replied, turning to the doors, "but right now, we're not in it. We're somewhere else."

Yaz stepped forward, desperate but hopeful. "Surely there's something we can do to fix it."

The Doctor shook her head doubtfully,

"I don't know. The last time this happened there was still some residual power," she kicked the TARDIS console in frustration, "but there's nothing! Absolutely nothing!"

Stepping back, the Doctor took a deep breath and tried to think.

"It was a long time ago and under different circumstances, the last time this happened I landed in a parallel universe. It was almost exactly the same to ours but with slight changes in the timeline."

"What, like alternate history type stuff?" Graham asked.

"I guess. Last time I was lucky enough to land in the equivalent of present day Earth. Maybe we've landed somewhere similar."

"Then let's have a look." Ryan said, trying to take charge of the demoralised group. He made his way to the doors and peered out the windows, trying to see if anything was visible outside. Grabbing the door handle, he was about to pull the door open when Graham stopped him.

"Open it slowly, mate. It looks quite bright out there." He gestured to the faint white glow through the murky windows.

Acknowledging, Ryan slowly pried the TARDIS door open and a harsh bright light flooded the large room. Squinting painfully as their eyes adjusted to the bright sun, the four cautiously inched out of the door one by one.

"It's times like this I miss my Sonic Sunglasses." The Doctor remarked, shielding her eyes.

"Your what?" Graham scoffed,

"It's a long story."

**MrWorthARead here. Once again, I have returned from months of inactivity with a new story for you all. With Season 12 of Doctor Who coming out swinging, I thought I'd jump on the bandwagon and drop a crossover story. Hope you enjoy ;)**


	2. City under siege

Chapter Two: City under Siege

They found themselves standing on a large boardwalk spanning off a great distance in either direction. On one side was the ocean, looking like it was a bay of some kind as various boats and shops could be seen docked off in the distance. On the other side was a mass of empty streets and a large skyline towering over them.

"Well, we're in a city. And it looks like earth." Yaz remarked.

"Better than stumbling out into a sun." Graham chuckled back, "That would have been nasty."

The Doctor still looked uncertain. Arms crossed, she thought long and hard. This was all familiar. They had landed on a parallel earth in the middle of a city. Part of her deep down was screaming what it was but she couldn't quite place it. It was over a thousand years ago. Except this was different, it wasn't London; the forest of silver skyscrapers was from somewhere else. Off in the distance, the Doctor could see the faint outline of a mountain just beyond the city. The huge snow-capped mount dwarfed the modern skyline.

"We're in Japan, I think." Graham spoke up, nodding to the various street signs and advertisements all the way up the street they were facing.

"Tokyo." The Doctor replied. "Tokyo in a parallel universe."

Ryan had clued onto something nobody else had,

"Where is everyone?"

The streets were completely empty. Not a single soul in sight. The city wasn't abandoned as everything seemed intact and there were no signs of things falling apart from neglect. It was recently lived in, but as if the entire population had just stopped what they were doing and left.

A jet screamed overhead, leaving a thin white vapour trail. Banking to one side, the aircraft arced to the left and dived at a small island out in the bay, letting out the distant crack of a missile launching. The four watched the tiny spec drop from the underside of the plane an streak through the air. The muffled explosion when it hit it's target startled everyone as they watched the fire blossom against the dark grey stone.

They were too focused on the explosion to see that it wasn't actually made of stone.

It moved.

Slowly at first, the massive object started to rise out of the water. More and more features became visible as water sloshed away. A clearly visible snout, jaws, followed by a neck, shoulders and arms. It's back was lined with rows of jagged white spikes and a long snakelike tail curled up behind it. The animal looked reptilian, resembling old artists' interpretations of dinosaurs as it stood up straight on hind legs.

It's roar was the loudest thing any of the Doctor's companions had ever heard.

More planes flew past, unloading their salvos on the beast as it strode up into the bay. The creature roared again, seemingly unfazed by the immense firepower wielded against it. Completely out of the water now, the animal marched onto dry land, leaving house-sized footprints in the earth as it towered as high as the skyscrapers it was heading towards.

"Now would be a good time to run." The Doctor said quietly, beginning to back away.

Ryan and Graham didn't question it and took off down the street.

"But what about the TARDIS?" Yaz yelled, breaking into a sprint alongside the Doctor.

"As long as he doesn't step directly on it, it should be fine!" The Doctor panted back, keeping her head up as she ran, the ends of her long coat flailing in the wind behind her.

The earth itself shook with each footfall of the immense beast as it shrugged off the last of the aircraft's barrage and laid siege to the city, clawing at the sides of buildings that got in it's way. Debris fell from the crippled structures, shattering into dust which washed harmlessly off the creature.

A building exploded behind the four as they ran, knocked over by the beast. Barely escaping the dust cloud, they had to get out of the creature's path. An opportunity came when there was an intersection on the street, with a road leading off to the right and up a hill.

"To the right! To the right!" the Doctor shouted, pointing in the direction leading out of the way of the pursuing monster. Both hearts pounding loudly in her ears, the Doctor guided the others up the street, passing parked cars and empty shops.

As luck would have it, the creature was not focussed on the four tiny fleeing people and continued it's path of mayhem deeper into the city. The doctor wanted a better view of the thing. Going into the entrance of a nearby building, the group passed through an empty hotel lobby and rushed to the elevator.

Pushing the button for the roof, the Doctor took out her sonic screwdriver and gave the elevator panel a buzz to speed up the ascent. The cables whirred and the tiny elevator was hurled up the building to the roof.

There was an awkward silence on the way up, which was quickly broken up by laughter. That was a close call. At least they were out of harm's way for now.

The elevator dinged when it reached the top and the doors opened. Taking the last flight of stairs to the roof, the Doctor undid the lock with her sonic and the team spilled out onto the flat open roof of the building.

Smoke bellowed up from the city in the distance as the monster continued to destroy buildings in it's warpath. Everyone had a better view of the creature from the rooftop. It roared again in the distance, trying to move further into to the city.

A connection finally twigged in the Doctor's mind. It wasn't connected to her original problem but it answered something from much further back in her history.

"Well that answers where _you_ got off to..." she said, staring off at the giant reptile.


	3. Machines of War

Chapter Three: Machines of War

"So let me get this straight," Graham started, "You actually _know _that great, big, city-destroying lizard?"

The Doctor nodded.

"His name is Godzilla. Short-tempered fella, but his heart is in the right place. I ran into him in the 1970s and he helped stop an alien invasion." She took a seat on nearby air duct, trying to explain the connection. "U.N.I.T. wasn't too happy with him stomping about in major cities, so I helped transport him to another universe under the condition he was good."

She glanced off at the horizon in time to see Godzilla tear down another building.

"He must of landed here. And from the looks of it, he seems to have forgotten shat i told him."

Suddenly, the rooftop they were on was cloaked in shadow as something massive slowly passed overhead. Gusts of wind kicked up and swirled as the team looked up to see a huge airship passing overhead.

It was the same general design as old wartime zeppelins, though fitted with modern crew compartments and engines. The underside was stamped with various markings, the easiest to make out reading;

_WARSHIP-03_

_JSDF_

More of the craft could be seen closing in around the city now. At least a half-dozen of them hovered into position around Godzilla. One by one, their weapons began firing. Crackling white hot beams of electricity fired from their canons, striking the monster one after the other.

It seemed to be working. The beast roared in pain, unable to shrug off these high-powered bolts of energy. The airships continued their barrage, taking turns firing to cover the others as they recharged their salvos.

With a defeated growl, Godzilla turned heel and started to retreat. Lurching back down the ruined city streets, Godzilla sulked back into the waters of the bay and as suddenly as he had arrived; he disappeared.

Having seen their foe off, the airships ceased firing and hovered in position, standing by for the order to return to base.

Ryan was awestruck at the spectacle. His adventures with the Doctor had let him see so many great things no other human would but nothing of the sheer scale that had just unfolded in front of him.

Yaz was the same, barely able to comprehend the battle and the immense devastation the creature left behind simply by coming up onto land.

As for Graham, it reminded him of the many cheesy monster movies from back when he was a kid. Late on Friday nights, he'd stay up and watch old 50's science fiction movies that would regularly come on. Except this time it wasn't a guy in a rubber suit knocking over cardboard buildings; it was real.

The rumbling of helicopter rotors caught the gang's attention as a military helicopter hovered above them. Having seen the four seemingly stranded on the roof, the helicopter started to descend, setting it's wheels down on an empty space of roof. The side doors slid open and a squad of soldiers spilled out.

"What are you doing here?" The squad leader barked, having to shout over the loud engines of the helicopter as he pushed his goggles up onto his helmet. "The city's supposed to have been completely evacuated!"

"We just got a bit lost, mate." Graham joked. "We're on holiday."

Both Ryan and Yaz sighed in embarrassment.

...

"Outstanding. Truly outstanding." General Ozaki exclaimed as he walked into the improvised command centre. The military had set up a forward command post in the Tokyo Tower, where the upper floors gave them a full 360 degree view of the city. Several miles further inland was their main base, both camps heavily guarded by an army of tanks and soldiers.

The general was being briefed on the success the army had in driving Godzilla off with the airships. A tall man in his late sixties, he war a green camouflaged uniform with the various striped denoting his rank. He had cold, stern eyes and a closely-shaved silver buzzcut. Ozaki was a veteran with many engagements under his belt from across the world. Right now, he was the supreme commander of military forces in Tokyo, with the fight against Godzilla being his top priority.

His subordinate officer struggled to keep pace as he strode across the room to the windows overlooking the city.

"Have the airships remain on station for the time being." He said, "just in case Godzilla wants to come back for round two." The officer acknowledged with the typical 'Yes, sir.' before snapping alert as information was being spoken into his earpiece.

"Sir, reports are just coming in from security," the officer said, two fingers on his earpiece as he listened to the updates, "One of our birds just found four civilians in the city and brought them here. One of them is calling themselves 'the Doctor'."

General Ozaki nodded in acknowledgment, not taking his eyes of the Tokyo skyline.

"Send them over to the science deck and inform Doctor Serizawa he has guests."

**hope you're enjoying it so far. Feel free to leave a review. **

**As always; stay epic**


	4. Another Doctor's Memories

Chapter Four: Another Doctor's Memories

The four time travellers were quickly headed into a large hangar by the soldiers who them promptly left. They had been picked up on the rooftop and flown over to the military base just outside the city after the Doctor identified herself and flashed the soldiers the psychic paper.

The hangar was filled with various disassembled machines and computers. A handful of men and women in lab coats worked at various stations as a trio of soldiers stood guard on the other side of the massive room.

When their guards left and closed the door, the sound caught one of the scientists' attention and he popped his head up over a computer. Quickly finishing what he was working on, the man hurried over to the group in an eccentric yet awkward dash.

"I'm Doctor Serizawa. Chief Researcher." He introduced himself eagerly, shaking everyone's hands. He was a man in his mid forties with long messy hair that was greying at the temples. One of his eyes was covered by an eyepatch and the bags under the other indicated he was incredibly overworked.

He turned to the Doctor,

"So you must be the Doctor? I've heard about your work in London before the War."

Pretending to know what he was talking about, the Doctor answered, talking about the technology they were using to drive off Godzilla.

"I reverse engineered it all myself." He explained, "Took what was left in the old company labs and warehouses and reworked it to help fight Godzilla."

He guided her over to a monitor, which showed various camera feeds of the city's defences being worked on by technicians.

"The airships are only the beginning. They're just refits of the old corporate ones you'd see hovering over major cities."

All of this was familiar in the Doctor's head but she couldn't quite put the pieces together. Parallel earth, corporate airships and her own involvement that helped saved the day.

_But what exactly happened?_

She listened to Serizawa's speech intently, hoping to have any clues seep through. Biting her lip, she struggled to remember and averted her gaze, looking back at the monitor with the camera feeds.

The footage showed scientists taking various machines apart and assembling others. _No that's not it._ She thought. It was staring her in the face and the Doctor knew it would jump out. It had to.

It was then that she recognised the insignia that everything was emblazoned with. It was a A C-shape cutout surrounded by a circle with a smaller circle orbiting in the bottom corner. The logo was hovering on the monitor's background with the company name:

_Cybus Industries_

The sounds of Serizawa talking faded away as a million memories came flooding back. A different time... a different life... It was back during one of her older regenerations: The Doctor and _his _companions were stuck in parallel-earth London. And then, not long later, the same threat returned, tearing through the void into his own world... _ending in the loss of a loved one..._

"Hey, Doc." Graham nudged her and she snapped back to the real world. "You okay in there?" She nodded, trying to focus on the present.

"Yeah I'm fine," she lied, hoping her uneasiness wasn't worrying the gang.

Serizawa rubbed his hands together, sighing.

"Today's been quite rough and we're all a bit shaken I think," he said, "The staff rec room is just around the corner. Make yourselves at home and I'll be there in a bit."

...

Yuko and Kazuma were just finishing their shifts soon. They had been disassembling one of the old Cybus transport pods. Serizawa had tasked them with experimenting with the machine's AI to see if it was capable of the same functions as the airship's controls. If it was possible, they could remove the need for human pilots and have the airships be operated autonomously.

Kazuma flipped up the visor on his welding mask, yawning.

"Are we in, yet?" He asked sleepily, "I'm sick of cutting open these pods and seeing those guys inside." He gestured to the deactivated silver humanoids stored in rows inside the container-sized transport pod.

"They freak me out."

"I know. They scare me too." Yuko replied from over by her computer. "I try to pretend they're not part-human in there."

"Same. Lumic was a twisted piece of crap to do this to people."

Yuko furrowed her brow while staring at the screen.

"Hang on, that's not right." She spun through console round so Kazuma could see.

"The AI on all of the pods aren't active but they're all emitting this low frequency that's able to connect them."

"Could it be to do with the other tech we've got hanging about this place?" Kazuma asked, flipping down his mask and resuming to cut through the control panel with his blowtorch.

Yuko's eyes darted frantically about the screen as something was going horribly wrong. The frequency wasn't just connecting the handful of pods in the room; it was connected to all of them, dotted across the base. She was seeing signs of activity, but not from the pod's AI. Each pod was beginning to light up with the vitals of its' dozen occupants. Yuko slowly backed away from the monitor, a look of pure horror on her face as she realised what was happening.

"Kazuma. Get away from that pod."

Switching off the blowtorch, he flipped up his mask and turned to her.

"What is it?

He didn't see the figure sitting up out of the pod behind him.

A bulky metal hand shot out of the pod and grabbed Kazuma, who helped in fright as he was pulled into the pod. A second hand dug it's' fingers into his shoulder and suddenly a thousand volts of electricity surged through his body. Unable to scream, Kazuma silently twitched and spasmed before going limp.

Trembling with fear, Yuko backed up into the corner of the room as one by one, the robotic figures rose from the pod like a vampire rising from a coffin. Their heavy footfalls, combined with the hisses of hydraulic joints echoed over each other as they filed out into the room, closing in on the tierrified scientist.

Yuko saw their faces; blank expressionless faceplates with lifeless black eyes.

She screamed as they closed in around her.

**And the big reveal (aside from Godzilla)!**

**So yeah, this is a spiritual successor to Rise of the Cybermen/Age of Steel and Army of Ghosts/Doomsday from season 2. **


End file.
